Pipeline for Staphylococcal Cassette Chromosome mec Classification

Prerequisites

• python 3.7
• virtualenv

Installing

Create working dir

$ mkdir workingspace
$ cd workingspace

Create a virtualenv & activate it

$ virtualenv sccmec_cla
$ source ./sccmec_cla/bin/activate

Download and unzip

$ unzip SCCmec_CLA-master.zip
$ cd SCCmec_CLA-master

Setup PROKKA database

$ ./helpers/programs/prokka-1.12/bin/prokka --setupdb

Install requirements

$ pip install -r requirements.txt

Usage

Put sequences (contigs files) inside INPUT folder and run

$ python sccmec_classification.py

OUTPUT

• attL_<CONTIG_FILENAME>.fasta <- left end sccmec
• attR_<CONTIG_FILENAME>.fasta <- right end sccmec
• sccmec_<CONTIG_FILENAME>.fasta <- cassette fasta format
• sccmec_<CONTIG_FILENAME>_type.txt <- current format annotation
• core_elements_sccmec_<CONTIG_FILENAME>.txt <- detail current format annotation
• annotation_table_sccmec_<CONTIG_FILENAME>.txt <- sccmec annotation table
• sccmec_<CONTIG_FILENAME>_neighbors_cassettes.txt <- close related cassettes
• fig.png <- network viz using matplotlib
• sccmec_<CONTIG_FILENAME>_cytoscape_network.sif <- Cytoscape format files
• sccmec_<CONTIG_FILENAME>_cytoscape_network.eda <- Cytoscape format files
• SCCmec_<CONTIG_FILENAME>.png <- Graphical Representation

Built With

• [prokka](add link) - Used to make annotation
• [BLAST](add link) - Used to identify core elements
• [mash](add link) - Used to generate similarity networks
• [DnaFeaturesViewer](add link) - Used create a graphical representation

Contributing

Versioning

Author

• Felipe Sepúlveda - Initial work - fesepc

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Ulab ugaldelab